Magnesium in PDB 7ljf: Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate (pdb code 7ljf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate, PDB code: 7ljf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:85.2 occ:1.00 O1A A:ATP702 2.0 113.0 1.0 O3B A:ATP702 2.0 113.0 1.0 OG1 A:THR300 2.0 57.1 1.0 O3A A:ATP702 2.2 113.0 1.0 O3G A:ATP702 2.2 113.0 1.0 PB A:ATP702 2.4 113.0 1.0 PG A:ATP702 2.5 113.0 1.0 PA A:ATP702 2.5 113.0 1.0 O2B A:ATP702 2.5 113.0 1.0 O2G A:ATP702 2.9 113.0 1.0 CB A:THR300 3.2 57.1 1.0 O5' A:ATP702 3.6 113.0 1.0 O2A A:ATP702 3.7 113.0 1.0 N A:THR300 3.8 57.1 1.0 O1B A:ATP702 3.8 113.0 1.0 O1G A:ATP702 3.9 113.0 1.0 CA A:THR300 4.1 57.1 1.0 CG A:LYS299 4.1 55.5 1.0 CG2 A:THR300 4.2 57.1 1.0 N A:LYS299 4.8 55.5 1.0 C5' A:ATP702 4.9 113.0 1.0 CD A:LYS299 4.9 55.5 1.0 C A:LYS299 4.9 55.5 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:85.0 occ:1.00 O1B B:ADP701 2.0 113.0 1.0 O1A B:ADP701 2.1 113.0 1.0 OG1 B:THR300 2.2 77.3 1.0 PA B:ADP701 2.3 113.0 1.0 PB B:ADP701 2.5 113.0 1.0 O2A B:ADP701 2.5 113.0 1.0 O3B B:ADP701 2.6 113.0 1.0 O3A B:ADP701 2.7 113.0 1.0 CB B:THR300 3.3 77.3 1.0 N B:THR300 3.8 77.3 1.0 O5' B:ADP701 3.9 113.0 1.0 O2B B:ADP701 4.0 113.0 1.0 CA B:THR300 4.1 77.3 1.0 CG2 B:THR300 4.4 77.3 1.0 OE2 B:GLU372 4.6 118.4 1.0 OD2 B:ASP371 4.6 104.6 1.0 CB B:LYS299 4.9 74.5 1.0 OD1 B:ASP371 4.9 104.6 1.0 C B:LYS299 4.9 74.5 1.0 N B:LYS299 4.9 74.5 1.0 C5' B:ADP701 4.9 113.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:127.0 occ:1.00 O3A C:ADP701 2.1 141.0 1.0 O1B C:ADP701 2.1 141.0 1.0 O1A C:ADP701 2.2 141.0 1.0 PA C:ADP701 2.5 141.0 1.0 PB C:ADP701 2.6 141.0 1.0 OG1 C:THR300 2.9 151.4 1.0 O2A C:ADP701 3.2 141.0 1.0 O2B C:ADP701 3.4 141.0 1.0 N C:THR300 3.8 151.4 1.0 CB C:LYS299 3.8 156.8 1.0 O3B C:ADP701 3.9 141.0 1.0 O5' C:ADP701 3.9 141.0 1.0 CB C:THR300 4.0 151.4 1.0 CG C:LYS299 4.4 156.8 1.0 C C:LYS299 4.5 156.8 1.0 CA C:THR300 4.5 151.4 1.0 CA C:LYS299 4.5 156.8 1.0 N C:LYS299 4.5 156.8 1.0 CD C:LYS299 4.6 156.8 1.0 OD1 C:ASP371 4.7 196.3 1.0 OD2 C:ASP371 4.9 196.3 1.0 C5' C:ADP701 4.9 141.0 1.0

Y.Yin, H.Li. Cryo-Em Structure of the Mpa Hexamer in the Presence of Atp and the Pup-Fabd Substrate J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X